BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524292.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,648,035 number of mapped reads = 1,533,713 (93.06%) number of supplementary alignments = 5,713 (0.35%) number of secondary alignments = 0 number of mapped bases = 90,831,642 bp number of sequenced bases = 90,803,783 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,414 duplication rate = 2.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7164 >>>>>>> ACTG content number of A's = 24,185,455 bp (26.63%) number of C's = 16,682,914 bp (18.37%) number of T's = 29,311,134 bp (32.28%) number of G's = 20,612,951 bp (22.7%) number of N's = 11,329 bp (0.01%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 436,748 number of insertions = 7,687 mapped reads with insertion percentage = 0.5% number of deletions = 17,614 mapped reads with deletion percentage = 1.14% homopolymer indels = 43.61% >>>>>>> Coverage mean coverageData = 0.0293X std coverageData = 0.2963X There is a 2.65% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7238752 0.02904206204565484 0.587986665928917 chr2 243199373 7732808 0.03179616750081013 0.2944602107559706 chr3 198022430 6138883 0.031000947720922323 0.19061334382849066 chr4 191154276 5946711 0.031109484571509142 0.20980541918542236 chr5 180915260 5634264 0.031143110868591183 0.19209039813620285 chr6 171115067 5328318 0.031138800886540283 0.20555528236682813 chr7 159138663 5037441 0.031654413233319675 0.4127396772215822 chr8 146364022 4688049 0.032030064054949244 0.28609819175825885 chr9 141213431 3562078 0.02522478191185653 0.25818221728403534 chr10 135534747 4357388 0.03214960072194623 0.2848607825816585 chr11 135006516 4230140 0.03133285803775575 0.2705197764653599 chr12 133851895 4017180 0.030012126462610037 0.19094678646612798 chr13 115169878 2941367 0.025539377579265995 0.17395364678253153 chr14 107349540 2802791 0.026109017327880492 0.1859288397687106 chr15 102531392 2578595 0.025149322072990095 0.1709034716265723 chr16 90354753 2528474 0.02798385160767359 0.2008650380535562 chr17 81195210 2286754 0.028163656452147856 0.20203392260366698 chr18 78077248 2474384 0.031691485847452 0.5076915636955459 chr19 59128983 1569357 0.026541247969713938 0.3929582343498712 chr20 63025520 1863528 0.029567832205113102 0.19017177495610305 chr21 48129895 1202451 0.024983453631054045 0.1937433817066032 chr22 51304566 1010123 0.01968875440833083 0.14976494441963673 chrMT 16571 18919 1.1416933196548187 1.2706161008779087 chrX 155270560 5365866 0.0345581673692682 0.2281746614330104 chrY 59373566 277021 0.0046657295268402775 0.12516106805309712